


@string{entcs = {ENTCS}}

@string{lncs = {LNCS}}

@string{tcs = {TCS}}



@article{Imlay03061988,
author = {Imlay, JA and Linn, S}, 
title = {DNA damage and oxygen radical toxicity},
volume = {240}, 
number = {4857}, 
pages = {1302-1309}, 
year = {1988}, 
doi = {10.1126/science.3287616}, 
URL = {http://www.sciencemag.org/content/240/4857/1302.abstract}, 
eprint = {http://www.sciencemag.org/content/240/4857/1302.full.pdf}, 
journal = {Science} 
}


@article{Elowitz,
	Author = {Michael Elowitz and Stanislas Leibler},
	Journal = {Nature},
	Number = {6767},
	Pages = {335-8},
	Title = {A Synthetic Oscillatory Network of Transcriptional Regulators},
	Volume = {403},
	Year = {2000}}

@inproceedings{uppaal,
	Author = {Gerd Behrmann and Alexandre David and Kim Guldstrand Larsen},
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Booktitle = {SFM},
	Crossref = {DBLP:conf/sfm/2004},
	Ee = {http://dx.doi.org/10.1007/978-3-540-30080-9_7},
	Pages = {200-236},
	Title = {A Tutorial on {UPPAAL}},
	Year = {2004}}

@proceedings{DBLP:conf/sfm/2004,
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Booktitle = {SFM},
	Editor = {Marco Bernardo and Flavio Corradini},
	Isbn = {3-540-23068-8},
	Publisher = {Springer},
	Series = lncs,
	Title = {Formal Methods for the Design of Real-Time Systems, International School on Formal Methods for the Design of Computer, Communication and Software Systems, SFM-RT 2004, Bertinoro, Italy, September 13-18, 2004, Revised Lectures},
	Volume = {3185},
	Year = {2004}}

@article{DBLP:journals/tcs/AlurD94,
	Author = {Rajeev Alur and David L. Dill},
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Ee = {http://dx.doi.org/10.1016/0304-3975(94)90010-8},
	Journal = tcs,
	Number = {2},
	Pages = {183-235},
	Title = {A Theory of Timed Automata},
	Volume = {126},
	Year = {1994}}

@inproceedings{DBLP:conf/dfg/EshuisW03,
	Author = {Rik Eshuis and Roel Wieringa},
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Booktitle = {Petri Net Technology for Communication-Based Systems},
	Crossref = {DBLP:conf/dfg/2003},
	Ee = {http://dx.doi.org/10.1007/978-3-540-40022-6_16},
	Pages = {321-351},
	Title = {Comparing Petri Net and Activity Diagram Variants for Workflow Modelling - A Quest for Reactive Petri Nets},
	Year = {2003}}

@proceedings{DBLP:conf/dfg/2003,
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Booktitle = {Petri Net Technology for Communication-Based Systems},
	Isbn = {3-540-20538-1},
	Publisher = {Springer},
	Series = lncs,
	Title = {Petri Net Technology for Communication-Based Systems - Advances in Petri Nets},
	Volume = {2472},
	Year = {2003}}

@inproceedings{Wang04formalverification,
	Author = {Farn Wang},
	Booktitle = {Proceedings of the IEEE},
	Pages = {2004},
	Title = {Formal verification of timed systems: A survey and perspective},
	Year = {2004}}

@inproceedings{Basso-Blandin2012,
	Author = {Adrien Basso-Blandin and Franck Delaplace},
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Booktitle = {MeCBIC},
	Crossref = {DBLP:journals/corr/abs-1211-3476},
	Ee = {http://dx.doi.org/10.4204/EPTCS.100.3},
	Pages = {29-47},
	Title = {GUBS, a behavior-based language for open system dedicated to synthetic biology},
	Year = 2012}

@article{AbdullaCJT00,
	Author = {Parosh Aziz Abdulla and Karlis Cerans and Bengt Jonsson and Yih-Kuen Tsay},
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Journal = {Information and Computation},
	Number = {1-2},
	Pages = {109-127},
	Title = {Algorithmic Analysis of Programs with Well Quasi-ordered Domains},
	Volume = 160,
	Year = 2000}

@article{afshari,
	Author = {Afshari, Cynthia A. and Hamadeh, Hisham K. and Bushel Pierre R.},
	Journal = {Toxicological Sciences},
	Number = 1,
	Pages = {225-237},
	Title = {The evolution of bioinformatics in toxicology: advancing toxicogenomics},
	Volume = 120,
	Year = 2011}

@article{Basso-Blandin2013,
	Author = {Adrien Basso-Blandin and Franck Delaplace},
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Ee = {http://dx.doi.org/10.7561/SACS.2013.1.1},
	Journal = {Sci. Ann. Comp. Sci.},
	Number = 1,
	Owner = {Franck},
	Pages = {1-38},
	Timestamp = {2014.01.03},
	Title = {GUBS, a Behaviour-Based Language for Design in Synthetic Biology},
	Volume = 23,
	Year = 2013}

@article{Beal2011,
	Author = {Beal, Jacob and Lu, Ting and Weiss, Ron},
	Doi = {10.1371/journal.pone.0022490},
	Editor = {Ben-Jacob, Eshel},
	File = {:C$\backslash$:/Users/Franck/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Beal, Lu, Weiss - 2011 - Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks.pdf:pdf},
	Issn = {1932-6203},
	Journal = {PLoS ONE},
	Number = 8,
	Pages = {e22490},
	Title = {{Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks}},
	Url = {http://dx.plos.org/10.1371/journal.pone.0022490},
	Volume = 6,
	Year = 2011,
	Bdsk-Url-1 = {http://dx.plos.org/10.1371/journal.pone.0022490},
	Bdsk-Url-2 = {http://dx.doi.org/10.1371/journal.pone.0022490}}

@article{Bilitchenko2011,
	Abstract = {Synthetic biological systems are currently created by
                  an ad-hoc, iterative process of specification, design,
                  and assembly. These systems would greatly benefit from
                  a more formalized and rigorous specification of the
                  desired system components as well as constraints on
                  their composition. Therefore, the creation of robust
                  and efficient design flows and tools is imperative. We
                  present a human readable language (Eugene) that allows
                  for the specification of synthetic biological designs
                  based on biological parts, as well as provides a very
                  expressive constraint system to drive the automatic
                  creation of composite Parts (Devices) from a
                  collection of individual Parts.},
	Author = {Bilitchenko, Lesia and Liu, Adam and Cheung, Sherine and Weeding, Emma and Xia, Bing and Leguia, Mariana and Anderson, J. Christopher and Densmore, Douglas},
	Doi = {10.1371/journal.pone.0018882},
	File = {:C$\backslash$:/Users/Franck/Dropbox/My Bibliography/Bilitchenko et al. - 2011 - Eugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems.pdf:pdf},
	Issn = {1932-6203},
	Journal = {PloS one},
	Number = 4,
	Pages = {e18882},
	Pmid = 21559524,
	Title = {{Eugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems.}},
	Url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3084710\&tool=pmcentrez\&rendertype=abstract},
	Volume = 6,
	Year = 2011,
	Bdsk-Url-1 = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3084710%5C&tool=pmcentrez%5C&rendertype=abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1371/journal.pone.0018882}}

@article{DBLP:journals/ijfcs/BrijderEMR11,
	Author = {Robert Brijder and Andrzej Ehrenfeucht and Michael G. Main and Grzegorz Rozenberg},
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Ee = {http://dx.doi.org/10.1142/S0129054111008842},
	Journal = {Journal of Foundations of Computer Science},
	Number = 7,
	Pages = {1499-1517},
	Title = {A Tour of reaction Systems},
	Volume = 22,
	Year = 2011}

@article{giavitto04a,
	Author = {J.-L. Giavitto and G. Malcolm and O. Michel},
	Equipe = {specif},
	Issue = 1,
	Journal = {Comparative and Functional Genomics},
	Kind = {intrevue},
	Month = feb,
	Pages = {95--99},
	Publisher = {Wiley},
	Title = {Rewriting systems and the modelling of biological systems},
	Volume = 5,
	Year = 2004}

@article{journals/tcsb/Cardelli05,
	Added-At = {2005-12-22T00:00:00.000+0100},
	Author = {Cardelli, Luca},
	Biburl = {http://www.bibsonomy.org/bibtex/20e3ebf1e17c6b782a59c09d0481fc406/dblp},
	Date = {2005-12-22},
	Description = {dblp},
	Editor = {Priami, Corrado and Merelli, Emanuela and Gonzalez, Pedro Pablo and Omicini, Andrea},
	Ee = {http://dx.doi.org/10.1007/11599128_10},
	Interhash = {2848be2cdd43ed54ccd19f1789eecc1c},
	Intrahash = {0e3ebf1e17c6b782a59c09d0481fc406},
	Isbn = {3-540-30883-0},
	Journal = {Transactions on Computational Systems Biology},
	Keywords = {dblp},
	Pages = {145-168},
	Publisher = {Springer},
	Series = lncs,
	Timestamp = {2005-12-22T00:00:00.000+0100},
	Title = {Abstract Machines of Systems Biology.},
	Url = {http://dblp.uni-trier.de/db/journals/tcsb/tcsb3.html#Cardelli05},
	Volume = 3737,
	Year = 2005,
	Bdsk-Url-1 = {http://dblp.uni-trier.de/db/journals/tcsb/tcsb3.html#Cardelli05}}

@article{thomas1973boolean,
	Author = {Thomas, Ren{\'e}},
	Journal = {Journal of theoretical biology},
	Pages = {565--583},
	Title = {Boolean formalisation of genetic control circuits},
	Volume = 42,
	Year = 1973}

@incollection{CardelliP09,
	Added-At = {2011-09-22T00:00:00.000+0200},
	Author = {Cardelli, Luca and Priami, Corrado},
	Biburl = {http://www.bibsonomy.org/bibtex/20fc143882c83b3491ee5002153805ca3/dblp},
	Booktitle = {The Fourth Paradigm},
	Editor = {Hey, Tony and Tansley, Stewart and Tolle, Kristin M.},
	Ee = {http://research.microsoft.com/en-us/collaboration/fourthparadigm/4th_paradigm_book_part2_cardelli_priami.pdf},
	Interhash = {f8cdc5cb772c91659a0405a009e3fb4b},
	Intrahash = {0fc143882c83b3491ee5002153805ca3},
	Isbn = {978-0982544204},
	Keywords = {dblp},
	Pages = {99-105},
	Publisher = {Microsoft Research},
	Timestamp = {2011-09-22T00:00:00.000+0200},
	Title = {Visualization in process algebra models of biological systems.},
	Url = {http://dblp.uni-trier.de/db/books/collections/4paradigm2009.html#CardelliP09},
	Year = 2009,
	Bdsk-Url-1 = {http://dblp.uni-trier.de/db/books/collections/4paradigm2009.html#CardelliP09}}

@article{Czar2009,
	Abstract = {Chemical synthesis of custom DNA made to order calls
                  for software streamlining the design of synthetic DNA
                  sequences. GenoCAD (www.genocad.org) is a free
                  web-based application to design protein expression
                  vectors, artificial gene networks and other genetic
                  constructs composed of multiple functional blocks
                  called genetic parts. By capturing design strategies
                  in grammatical models of DNA sequences, GenoCAD guides
                  the user through the design process. By successively
                  clicking on icons representing structural features or
                  actual genetic parts, complex constructs composed of
                  dozens of functional blocks can be designed in a
                  matter of minutes. GenoCAD automatically derives the
                  construct sequence from its comprehensive libraries of
                  genetic parts. Upon completion of the design process,
                  users can download the sequence for synthesis or
                  further analysis. Users who elect to create a personal
                  account on the system can customize their workspace by
                  creating their own parts libraries, adding new parts
                  to the libraries, or reusing designs to quickly
                  generate sets of related constructs.},
	Author = {Czar, Michael J. and Cai, Yizhi and Peccoud, Jean},
	Doi = {10.1093/nar/gkp361},
	File = {:C$\backslash$:/Users/Franck/Dropbox/My Bibliography/Czar, Cai, Peccoud - 2009 - Writing DNA with GenoCAD.pdf:pdf},
	Issn = {1362-4962},
	Journal = {Nucleic acids research},
	Keywords = {Base Sequence,DNA,DNA: chemical synthesis,DNA: chemistry,Genes, Synthetic,Genetic Engineering,Software,User-Computer Interface},
	Number = {Web Server issue},
	Pages = {W40--7},
	Pmid = 19429897,
	Title = {{Writing DNA with GenoCAD.}},
	Url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2703884\&tool=pmcentrez\&rendertype=abstract},
	Volume = 37,
	Year = 2009,
	Bdsk-Url-1 = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2703884%5C&tool=pmcentrez%5C&rendertype=abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/nar/gkp361}}

@article{DBLP:journals/tcs/DanosL04,
	Author = {Vincent Danos and Cosimo Laneve},
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Ee = {http://dx.doi.org/10.1016/j.tcs.2004.03.065},
	Journal = tcs,
	Number = 1,
	Pages = {69-110},
	Title = {Formal molecular biology},
	Volume = 325,
	Year = 2004}

@incollection{DeCristofaro2008,
	Author = {DeCristofaro, MarcF. and Daniels, KellyeK.},
	Booktitle = {Essential Concepts in Toxicogenomics},
	Doi = {10.1007/978-1-60327-048-9_9},
	Editor = {Mendrick, DonnaL. and Mattes, WilliamB.},
	Isbn = {978-1-58829-638-2},
	Keywords = {biomarker; blood; gene expression; heart; kidney; molecular profiling; toxicogenomics; transcriptomics},
	Owner = {Franck},
	Pages = {185-194},
	Publisher = {Humana Press},
	Series = {Methods in Molecular Biology{\texttrademark}},
	Timestamp = {2014.01.02},
	Title = {Toxicogenomics in Biomarker Discovery},
	Url = {http://dx.doi.org/10.1007/978-1-60327-048-9_9},
	Volume = 460,
	Year = 2008,
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-1-60327-048-9_9}}

@article{Ehrenfeucht2007,
	Author = {Andrzej Ehrenfeucht and Grzegorz Rozenberg},
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Ee = {http://dx.doi.org/10.1016/j.tcs.2007.01.008},
	Journal = tcs,
	Number = {1-2},
	Pages = {3-16},
	Title = {Events and modules in reaction systems},
	Volume = 376,
	Year = 2007}

@article{emerson,
	Author = {E.Allen Emerson and Edmund M. Clarke},
	Journal = {Science of Comp. Programming},
	Number = 3,
	Pages = {241 - 266},
	Title = {Using branching time temporal logic to synthesize synchronization skeletons},
	Volume = 2,
	Year = 1982}

@article{FinkelS01,
	Author = {Alain Finkel and Philippe Schnoebelen},
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Ee = {http://dx.doi.org/10.1016/S0304-3975(00)00102-X},
	Journal = tcs,
	Number = {1-2},
	Pages = {63-92},
	Title = {Well-structured transition systems everywhere!},
	Volume = 256,
	Year = 2001}

@article{Foster2007,
	Abstract = {Toxicogenomics is considered a valuable tool for
                  reducing pharmaceutical candidate attrition by
                  facilitating earlier identification, prediction and
                  understanding of toxicities. A retrospective
                  evaluation of 3 years of routine transcriptional
                  profiling in non-clinical safety studies was
                  undertaken to assess the utility of toxicogenomics in
                  drug safety assessment. Based on the analysis of
                  studies with 33 compounds, marked global
                  transcriptional changes (> 4\% transcripts at p <
                  0.01) were shown to be a robust biomarker for dosages
                  considered to be toxic . In general, there was an
                  inconsistent correlation between transcription and
                  histopathology, most likely due to differences in
                  sensitivity to focal microscopic lesions, to secondary
                  effects, and to events that precede structural tissue
                  changes. For 60\% of toxicities investigated with
                  multiple time-point data, transcriptional changes were
                  observed prior to changes in traditional study
                  endpoints.  Candidate transcriptional markers of
                  pharmacologic effects were detected in 40\% of targets
                  profiled. Mechanistic classification of toxicity was
                  obtained for 30\% of targets. Furthermore, data
                  comparison to compendia of transcriptional changes
                  provided assessments of the specificity of
                  transcriptional responses. Overall, our experience
                  suggests that toxicogenomics has contributed to a
                  greater understanding of mechanisms of toxicity and to
                  reducing drug attrition by empiric analysis where
                  safety assessment combines toxicogenomic and
                  traditional evaluations.},
	Author = {Foster, William R and Chen, Shen-Jue and He, Aiqing and Truong, Amy and Bhaskaran, Vasanthi and Nelson, David M and Dambach, Donna M and Lehman-McKeeman, Lois D and Car, Bruce D},
	Doi = {10.1080/01926230701419063},
	File = {:C$\backslash$:/Users/Franck/Dropbox/My Bibliography/Toxicol Pathol-2007-Foster-621-35.pdf:pdf},
	Issn = {0192-6233},
	Journal = {Toxicologic pathology},
	Keywords = {Animals,Biological Markers,Dose-Response Relationship, Drug,Drug-Related Side Effects and Adverse Reactions,Gene Expression Profiling,Humans,Retrospective Studies,Risk Assessment,Safety,Toxicogenetics},
	Mendeley-Groups = {Articles/article-toxico},
	Month = aug,
	Number = 5,
	Owner = {Franck},
	Pages = {621--35},
	Pmid = 17654404,
	Timestamp = {2014.01.03},
	Title = {{A retrospective analysis of toxicogenomics in the safety assessment of drug candidates.}},
	Url = {http://www.ncbi.nlm.nih.gov/pubmed/17654404},
	Volume = 35,
	Year = 2007,
	Bdsk-Url-1 = {http://www.ncbi.nlm.nih.gov/pubmed/17654404},
	Bdsk-Url-2 = {http://dx.doi.org/10.1080/01926230701419063}}

@book{DBLP:series/eatcs/Jensen92,
	Author = {Kurt Jensen},
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Ee = {http://dx.doi.org/10.1007/978-3-662-06289-0},
	Isbn = {978-3-662-06291-3, 978-3-662-06289-0},
	Pages = {I-X, 1-236},
	Publisher = {Springer},
	Series = {EATCS Monographs on TCS},
	Title = {Coloured Petri Nets - Basic Concepts, Analysis Methods and Practical Use - Volume 1},
	Year = 1992}

@article{kavlock,
	Author = {Kavlock, Robert J. and Ankley, Gerald and Blancato, Jerry and Breen, Michael and Conolly, Rory and Dix, David and Houck, Keith and Hubal, Elaine and Judson, Richard and Rabinowitz, James and Richard, Ann and Setzer, Woodrow and Shah, Imran and Villeneuve, Daniel and Weber, Eric},
	Journal = {Toxicological Sciences},
	Number = 1,
	Pages = {14-27},
	Title = {Computational toxicology--a state of the science mini review},
	Volume = 103,
	Year = 2008}

@incollection{MadhuKrithi,
	Author = {Madhu, Mutyam and Krithivasan, Kamala},
	Booktitle = {Membrane Computing},
	Doi = {10.1007/3-540-36490-0_24},
	Editor = {P{\u A}un, Gheorghe and Rozenberg, Grzegorz and Salomaa, Arto and Zandron, Claudio},
	Isbn = {978-3-540-00611-4},
	Language = {English},
	Pages = {360-370},
	Publisher = {Springer Berlin Heidelberg},
	Series = lncs,
	Title = {A Survey of Some Variants of P Systems},
	Url = {http://dx.doi.org/10.1007/3-540-36490-0_24},
	Volume = 2597,
	Year = 2003,
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/3-540-36490-0_24}}

@article{computational,
	Abstract = {{ Computational systems biology is an emerging field
                  in biological simulation that attempts to model or
                  simulate intra- and intercellular events using data
                  gathered from genomic, proteomic or metabolomic
                  experiments. The need to model complex temporal and
                  spatiotemporal processes at many different scales has
                  led to the emergence of numerous techniques, including
                  systems of differential equations, Petri nets,
                  cellular automata simulators, agent-based models and
                  pi calculus.  This review provides a brief summary and
                  an assessment of most of these approaches. It also
                  provides examples of how these methods are being used
                  to facilitate drug discovery and development. }},
	Address = {National Research Council, National Institute for Nanotechnology (NINT) Edmonton, Alberta, Canada T6G 2E8.},
	Author = {Materi, Wayne and Wishart, David S.},
	Doi = {10.1016/j.drudis.2007.02.013},
	Issn = 13596446,
	Journal = {Drug Discovery Today},
	Keywords = {rev},
	Number = {7-8},
	Pages = {295--303},
	Pmid = 17395089,
	Posted-At = {2011-11-12 01:25:57},
	Priority = 2,
	Title = {{Computational systems biology in drug discovery and development: methods and applications}},
	Url = {http://dx.doi.org/10.1016/j.drudis.2007.02.013},
	Volume = 12,
	Year = 2007,
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.drudis.2007.02.013}}

@article{toxicogenomics,
	Author = {Nuwaysir, EF and Bittner, M and Trent, J and Barrett, JC and Afshari, CA},
	Journal = {Molecular Carcinogenesis},
	Number = 3,
	Pages = {153-159},
	Title = {Microarrays and toxicology: the advent of toxicogenomics},
	Volume = 24,
	Year = {1999}}

@article{DBLP:journals/ijfcs/PaunPRS11,
	Author = {Andrei Paun and Mihaela Paun and Alfonso Rodr\'{\i}guez-Pat{\'o}n and Manuela Sidoroff},
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Ee = {http://dx.doi.org/10.1142/S0129054111007812},
	Journal = {Int. Journal of Foundations of Computer Science},
	Number = 1,
	Pages = {39-53},
	Title = {P Systems with proteins on Membranes: a Survey.},
	Volume = 22,
	Year = 2011}

@article{Pennie2000,
	Author = {Pennie, WD and Tugwood, JD},
	Journal = {Toxicological pathology},
	Owner = {Franck},
	Pages = {277--283},
	Timestamp = {2014.01.02},
	Title = {{The principles and practice of toxicogenomics: applications and opportunities}},
	Url = {http://toxsci.oxfordjournals.org/content/54/2/277.short},
	Volume = 283,
	Year = 2000,
	Bdsk-Url-1 = {http://toxsci.oxfordjournals.org/content/54/2/277.short}}

@article{pinney,
	Abstract = {{The mathematical structures known as Petri Nets have
                  recently become the focus of much research effort in
                  both the structural and quantitative analysis of all
                  kinds of biological networks. This review provides a
                  very brief summary of these interesting new research
                  directions.}},
	Address = {Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K. john@bioinformatics.leeds.ac.uk},
	Author = {Pinney, J. W. and Westhead, D. R. and McConkey, G. A.},
	Citeulike-Article-Id = 273,
	Citeulike-Linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/14641101},
	Citeulike-Linkout-1 = {http://www.hubmed.org/display.cgi?uids=14641101},
	Issn = {0300-5127},
	Journal = {Biochemical Society Transactions},
	Keywords = {biology, net, petri, sysbio},
	Number = {Pt 6},
	Pages = {1513--1515},
	Pmid = 14641101,
	Posted-At = {2008-01-27 19:38:47},
	Priority = 2,
	Title = {{Petri Net representations in systems biology.}},
	Url = {http://view.ncbi.nlm.nih.gov/pubmed/14641101},
	Volume = 31,
	Year = 2003,
	Bdsk-Url-1 = {http://view.ncbi.nlm.nih.gov/pubmed/14641101}}

@article{Purnick2009,
	Abstract = {Synthetic biology is a research field that combines
                  the investigative nature of biology with the
                  constructive nature of engineering. Efforts in
                  synthetic biology have largely focused on the creation
                  and perfection of genetic devices and small modules
                  that are constructed from these devices. But to view
                  cells as true 'programmable' entities, it is now
                  essential to develop effective strategies for
                  assembling devices and modules into intricate,
                  customizable larger scale systems. The ability to
                  create such systems will result in innovative
                  approaches to a wide range of applications, such as
                  bioremediation, sustainable energy production and
                  biomedical therapies.},
	Author = {Purnick, Priscilla E M and Weiss, Ron},
	Doi = {10.1038/nrm2698},
	File = {:C$\backslash$:/Users/Franck/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Purnick, Weiss - 2009 - The second wave of synthetic biology from modules to systems.pdf:pdf},
	Issn = {1471-0080},
	Journal = {Nature reviews. Molecular cell biology},
	Keywords = {bsao},
	Mendeley-Tags = {bsao},
	Number = 6,
	Pages = {410--22},
	Pmid = 19461664,
	Shorttitle = {Nat Rev Mol Cell Biol},
	Title = {{The second wave of synthetic biology: from modules to systems.}},
	Url = {http://www.ncbi.nlm.nih.gov/pubmed/19461664},
	Volume = 10,
	Year = 2009,
	Bdsk-Url-1 = {http://www.ncbi.nlm.nih.gov/pubmed/19461664},
	Bdsk-Url-2 = {http://dx.doi.org/10.1038/nrm2698}}

@article{toxicology,
	Author = {Schmidt, Markus and Pei, Lei},
	Journal = {Toxicological sciences : an official journal of the Society of Toxicology},
	Number = 120,
	Pages = {S204-24},
	Title = {Synthetic toxicology: where engineering meets biology and toxicology},
	Volume = {Suppl. 1},
	Year = 2011}

@article{synthetic,
	Author = {Serrano, Luis},
	Journal = {Molecular Systems Biology},
	Number = 158,
	Title = {Synthetic biology: promises and challenges},
	Volume = 3,
	Year = 2007}

@article{DBLP:journals/tcs/CeroneM99,
	Author = {Antonio Cerone and Andrea Maggiolo-Schettini},
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Ee = {http://dx.doi.org/10.1016/S0304-3975(98)00008-5},
	Journal = tcs,
	Number = {1-2},
	Pages = {1-53},
	Title = {Time-Based Expressivity of Time Petri Nets for System Specification},
	Volume = 216,
	Year = 1999}

@inproceedings{FP-PNSE-2013,
	Abstract = {This paper presents Neco that is a Petri net
                  compiler: it takes a Petri net as its input and
                  produces as its output an optimised library to
                  efficiently explore the state space of this Petri
                  net. Neco is also able to work with LTL formulae and
                  to perform model-checking by using SPOT library. We
                  describe the components of Neco, and in particular
                  the exploration libraries it produces, with the aim
                  that one can use Neco in one's own projects in order
                  to speedup Petri nets executions.},
	Author = {Fronc, {\L}ukasz and Pommereau, Franck},
	Booktitle = {Proceedings of PNSE'13},
	Keywords = {Petri nets compilation, Optimised transition firing, Tools development, Explicit state space exploration},
	Month = {06},
	Pages = {1-7},
	Title = {Building {Petri} nets tools around {Neco} compiler},
	Year = {2013}}

@article{Pom-PNN-2008,
	Abstract = {This paper presents the toolkit SNAKES that is aimed
                  at providing a flexible solution to the problem of
                  quickly prototyping Petri nets tools. In particular,
                  SNAKES is expected to have as few built-in limitations
                  as possible with respect to the particular variant of
                  Petri net to be used. The goal is to make SNAKES
                  suitable for any kind of Petri net model, including
                  new ones for which there exists no available tool. For
                  this purpose, SNAKES is designed as a very general
                  Petri net core library enriched with a set of
                  extension modules to provide specialised features. On
                  the one hand, the core library is versatile in that it
                  defines a general Petri net structure where all the
                  computational aspects are delegated to an interpreted
                  programming language. On the other hand, extension
                  modules provide with enough flexibility to allow to
                  redefine easily any part of the base Petri net
                  model. In particular, SNAKES comes with a handful of
                  extension modules in order to handle models of the
                  Petri Box Calculus and M-nets family. SNAKES is
                  released under the GNU LGPL, it can be downloaded,
                  together with API documentation and a tutorial, at
                  \href{http://lacl.univ-paris12.fr/pommereau/soft/snakes}
                  {http://lacl.univ-paris12.fr/pommereau/soft/snakes}.},
	Author = {Pommereau, Franck},
	Journal = {Petri net newsletter},
	Keywords = {Petri nets, Quick prototyping},
	Month = 10,
	Note = {\href{http://www.ibisc.univ-evry.fr/~fpommereau/SNAKES} {SNAKES is available here}.},
	Number = {10-2008},
	Pages = {1-18},
	Title = {Quickly prototyping {Petri} nets tools with {SNAKES}},
	Year = 2008}

@article{DBLP:journals/entcs/ThanhKP02,
	Author = {C{\'e}cile Bui Thanh and Hanna Klaudel and Franck Pommereau},
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Ee = {http://dx.doi.org/10.1016/S1571-0661(04)80521-8},
	Journal = entcs,
	Number = 5,
	Pages = {85-100},
	Title = {{P}etri nets with causal time for system verification},
	Volume = 68,
	Year = 2002}

@book{Voigt2011,
	Author = {Voigt, C.},
	Isbn = 9780123851208,
	Owner = {Franck},
	Publisher = {Elsevier/Academic Press},
	Series = {Academic Press},
	Timestamp = {2014.01.04},
	Title = {Synthetic Biology: Computer Aided Design and DNA Assembly},
	Url = {http://books.google.fr/books?id=EJXBAXJYC1oC},
	Year = 2011,
	Bdsk-Url-1 = {http://books.google.fr/books?id=EJXBAXJYC1oC}}

@article{Waters2004,
	Abstract = {Toxicogenomics combines transcript, protein and
                  metabolite profiling with conventional toxicology to
                  investigate the interaction between genes and
                  environmental stress in disease causation. The
                  patterns of altered molecular expression that are
                  caused by specific exposures or disease outcomes have
                  revealed how several toxicants act and cause
                  disease. Despite these success stories, the field
                  faces noteworthy challenges in discriminating the
                  molecular basis of toxicity. We argue that toxicology
                  is gradually evolving into a systems toxicology that
                  will eventually allow us to describe all the
                  toxicological interactions that occur within a living
                  system under stress and use our knowledge of
                  toxicogenomic responses in one species to predict the
                  modes-of-action of similar agents in other species.},
	Author = {Waters, Michael D and Fostel, Jennifer M},
	Doi = {10.1038/nrg1493},
	File = {:C$\backslash$:/Users/Franck/Dropbox/My Bibliography/tox\_ReviewToxicogenomicsNaturedec2004.pdf:pdf},
	Issn = {1471-0056},
	Journal = {Nature reviews. Genetics},
	Keywords = {Animals,Computational Biology,Databases, Factual,Ecology,Forecasting,Gene Expression Profiling,Genetic Predisposition to Disease,Humans,Proteomics,Systems Theory,Toxicogenetics,Toxicology},
	Month = dec,
	Number = 12,
	Owner = {Franck},
	Pages = {936--48},
	Pmid = 15573125,
	Timestamp = {2014.01.02},
	Title = {{Toxicogenomics and systems toxicology: aims and prospects.}},
	Url = {http://www.ncbi.nlm.nih.gov/pubmed/15573125},
	Volume = 5,
	Year = 2004,
	Bdsk-Url-1 = {http://www.ncbi.nlm.nih.gov/pubmed/15573125},
	Bdsk-Url-2 = {http://dx.doi.org/10.1038/nrg1493}}

@proceedings{DBLP:journals/corr/abs-1211-3476,
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Booktitle = {MeCBIC},
	Editor = {Gabriel Ciobanu},
	Ee = {http://dx.doi.org/10.4204/EPTCS.100},
	Series = {EPTCS},
	Title = {Proceedings 6th Workshop on Membrane Computing and Biologically Inspired Process Calculi},
	Volume = 100,
	Year = 2012}

@article{kripke,
	Author = {Saul Kripke},
	Journal = {Acta Philosophica Fennica},
	Pages = {83--94},
	Title = {Semantical Considerations on Modal Logic},
	Volume = 16,
	Year = 1963}

@book{edmund,
	Author = {Edmund M. Clarke and Orna Grumberg and Doron Peled},
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Ee = {http://books.google.de/books?id=Nmc4wEaLXFEC},
	Isbn = {978-0-262-03270-4},
	Pages = {I-XIV, 1-314},
	Publisher = {MIT Press},
	Title = {Model checking},
	Year = 2001}

@inproceedings{DBLP:conf/birthday/BrijderER11,
	Author = {Robert Brijder and Andrzej Ehrenfeucht and Grzegorz Rozenberg},
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Booktitle = {Computation, Cooperation, and Life},
	Crossref = {DBLP:conf/birthday/2011paun},
	Ee = {http://dx.doi.org/10.1007/978-3-642-20000-7_16},
	Pages = {191-202},
	Title = {Reaction Systems with Duration},
	Year = 2011}

@proceedings{DBLP:conf/birthday/2011paun,
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Booktitle = {Computation, Cooperation, and Life},
	Editor = {Jozef Kelemen and Alica Kelemenov{\'a}},
	Ee = {http://dx.doi.org/10.1007/978-3-642-20000-7},
	Isbn = {978-3-642-19999-8},
	Publisher = {Springer},
	Series = lncs,
	Title = {Computation, Cooperation, and Life - Essays Dedicated to Gheorghe Paun on the Occasion of His 60th Birthday},
	Volume = 6610,
	Year = 2011}

@inproceedings{timestamp,
	Author = {Hans-Michael Hanisch and Kurt Lautenbach and Carlo Simon and Jan Thieme},
	Booktitle = {WODES '98},
	Pages = {321-326},
	Title = {Timestamp Petri Nets in Technical Applications},
	Year = 1998}

@inproceedings{koutnyreaction,
	Author = {Jetty Kleijn and Maciej Koutny and Grzegorz Rozenberg},
	Booktitle = {BioPPN-2011},
	Pages = {36-52},
	Title = {Modelling Reaction Systems with Petri Nets},
	Year = 2011}

@article{DBLP:journals/nc/ChaouiyaNRT11,
	Author = {Claudine Chaouiya and Aur{\'e}lien Naldi and Elisabeth Remy and Denis Thieffry},
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Ee = {http://dx.doi.org/10.1007/s11047-010-9178-0},
	Journal = {Natural Computing},
	Number = 2,
	Pages = {727-750},
	Title = {Petri net representation of multi-valued logical regulatory graphs},
	Volume = 10,
	Year = 2011}

@article{DBLP:journals/fuin/KleijnK11,
	Author = {Jetty Kleijn and Maciej Koutny},
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Ee = {http://dx.doi.org/10.3233/FI-2011-539},
	Journal = {Fundam. Inform.},
	Number = {1-4},
	Pages = {217-230},
	Title = {Membrane Systems with Qualitative Evolution Rules},
	Volume = 110,
	Year = 2011}

@article{giavitto2008,
	Abstract = {{Spatial computing is an emerging field that
                  recognizes the importance of explicitly handling
                  spatial relationships at three levels: computer
                  architectures, programming languages and
                  applications. In this context, we present MGS, an
                  experimental programming language where data
                  structures are fields on abstract spaces. In MGS,
                  fields are transformed using rules. We show that this
                  approach is able to unify, at least for programming
                  purposes, several computational models like
                  Lindenmayer systems and cellular automata. The MGS
                  notions of topological collection and transformation
                  are formalized using concepts developed in algebraic
                  topology. We propose to use transformations in order
                  to implement a discrete version of some differential
                  operators. These transformations satisfy a Stokes-like
                  theorem. This result constitutes a geometric view of
                  programming where data are handled like fields in
                  physics. The relevance of this approach for the design
                  of autonomic software systems is discussed in the
                  conclusion.}},
	Affiliation = {Informatique, Biologie Int{\'e}grative et Syst{\`e}mes Complexes - IBISC , ABC (Apprentissage et Biologie Computationnelle) - LORIA},
	Audience = {internationale},
	Author = {Giavitto, Jean-Louis and Spicher, Antoine},
	Doi = {10.1016/j.physd.2008.03.039},
	Hal_Id = {hal-00340126},
	Journal = {Physica D: Nonlinear Phenomena},
	Keywords = {Spatial computing; Data fields; Topological collection; Topological rewriting; Discrete differential operators; Declarative language},
	Language = {Anglais},
	Month = Jul,
	Number = {9},
	Pages = {1302--1314},
	Title = {{Topological Rewriting and the Geometrization of Programming}},
	Url = {http://hal.archives-ouvertes.fr/hal-00340126},
	Volume = 237,
	Year = 2008,
	Bdsk-Url-1 = {http://hal.archives-ouvertes.fr/hal-00340126},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.physd.2008.03.039}}

@article{Giavitto2012,
	Acknowledgement = ack-nhfb,
	Author = {Jean-Louis Giavitto and Hanna Klaudel and Franck Pommereau},
	Bibdate = {Fri Apr 6 10:37:33 MDT 2012},
	Bibsource = {http://www.math.utah.edu/pub/tex/bib/tcs2010.bib},
	Coden = {TCSCDI},
	Day = {4},
	Doi = {http://dx.doi.org/10.1016/j.tcs.2011.12.054},
	Fjournal = {Theoretical Computer Science},
	Issn = {0304-3975 (print), 1879-2294 (electronic)},
	Issn-L = {0304-3975},
	Journal = tcs,
	Journal-Url = {http://www.sciencedirect.com/science/journal/03043975/},
	Month = may,
	Number = {1},
	Pages = {219--234},
	Title = {Integrated regulatory networks {(IRNs)}: {Spatially} organized biochemical modules},
	Url = {http://www.sciencedirect.com/science/article/pii/S0304397511010206},
	Volume = {431},
	Year = {2012},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0304397511010206},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.tcs.2011.12.054}}
